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A community effort to collect a curated set of analysis pipelines built using Nextflow.
For facilities
Highly optimised pipelines with excellent reporting. Validated releases ensure reproducibility.
For users
Portable, documented and easy to use workflows.
Pipelines that you can trust.
For developers
Companion templates and tools help to validate your code and simplify common tasks.
Nextflow is an incredibly powerful and flexible workflow language.
nf-core pipelines adhere to strict guidelines - if one works, they all will.
Fully featured pipelines
Documentation
Extensive documentation covering installation, usage and description of output files ensures that you won't be left in the dark.
Portable and reproducible
Pipelines follow best-practices to ensure maximum portability and reproducibility. The large community makes the pipelines exceptionally well tested and easy to run.
Stable Releases
nf-core pipelines use GitHub releases to tag stable versions of the code and software, making pipeline runs totally reproducible.
CI Testing
Every time a change is made to the pipeline code, nf-core pipelines use continuous-integration testing to ensure that nothing has broken.
Cloud-ready
Pipelines are tested on AWS after every release. You can even browse results live on the website and use outputs for your own benchmarking.
Packaged software
Pipeline dependencies are automatically downloaded and handled using Docker, Singularity, Conda or others. No need for any software installations.
Developers: Not just another registry
Develop with the community
Come and talk to us before you start writing a pipeline to find collaborators and check that your pipeline is suitable for nf-core.
Start from the template
All pipelines, modules and subworkflows must be based on our template and be created using
nf-core tools. An automated sync keeps pipelines up to date.
Collaborate, don't duplicate
We only allow one pipeline per data type / analysis type. If a similar pipeline exists we'll ask you to add to that instead of making a new workflow.
Upcoming Events
Get started in minutes
Nextflow lets you run nf-core pipelines on virtually any computing environment.
Most nf-core genomics pipelines come with built-in support for AWS-iGenomes, with genome references for over 30 common species.
The nf-core companion tool makes it easy to list all available nf-core pipelines and shows which are available locally. Local versions are checked against the latest available release.
# Install nextflow
curl -s https://get.nextflow.io | bash
mv nextflow ~/bin/
# Launch the RNAseq pipeline
nextflow run nf-core/rnaseq \
--input samplesheet.csv \
--output ./results/ \
--genome GRCh37 \
-profile docker
# Install nf-core tools
pip install nf-core
# List all nf-core pipelines and show available updates
nf-core listSee what's available
Check out the available pipelines to see if we have what you need. Each comes with release details, keywords and a description.
Available pipelinesRun a pipeline
Read the quickstart tutorial to learn how to get set up with the required software and tools, and how to launch a nf-core pipeline.
Quickstart TutorialGet into the code
If you're interested in contributing to nf-core, take a look at the developer documentation to see what's required.
Developer docsSee a complete list » Used by groups all over the world
The nf-core community is spread all over the globe and includes a large number of contributing users.
